EPI2ME

Understanding Male Infertility Causes through Long-Read Sequencing

Thomas Garcia from Baylor College of Medicine spoke at the Nanopore Community Meeting in Boston on “Long-read sequencing for comprehensive profiling of infertile men.” There are pre and post-testicular causes of infertility, Garcia mentioned. Pre-testicular causes include Kallmann syndrome, Beta thalassemia, and sickle disease. Intrinsic testicular causes of infertility include chromosomal abnormalities, Y-chromosome microdeletions/duplications, and […]
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Understanding CoNS-seq: A Breakthrough in Viral Safety

Charles A. Swofford from the MIT Center for Biomedical Innovation presented as part of the Biopharma Day in Boston. The title of the session was “A sensitive sample preparation pipeline for adventitious virus detection using nanopore sequencing.” They emphasized the importance of viral safety assurance for biologics. The two assays used are in vivo virus […]
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Enhancing Single-Cell Analysis with EPI2ME

Individual cell analysis is possible with Oxford Nanopore Technologies (ONT). Matt Parker from ONT spoke about “Individual cells matter – single-cell data analysis with EPI2ME.” EPI2ME cloud was launched, and cloud-based analyses are possible. I have been testing and mentioning the new version in the Portable Genome Sequencing course. Bryan Leland, a Bioinformatics Manager with […]
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Latest EPI2ME Features for Variant Analysis Explained

Matt Parker, the Director of Clinical Bioinformatics Software at Oxford Nanopore Technologies, facilitated the Nanopore Community Meeting Boston 2024 session on variant analysis with EPI2ME. The title of the presentation was “Ultra-rich human data – variant analysis with EPI2ME.” They shared the EPI2ME user interface updates that were recently released. There is a new element […]
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Understanding the NO-MISS Workflow for Microbial Sequencing

Tonight, I watched the second half of a new Knowledge Exchange session focusing on “Sequencing and analysis of nanopore-only microbial isolates with the NO-MISS workflow.” Different extraction methods produced varying yields. Bead-beating and enzymatic lysis extractions affect read length and throughput, while fungal samples produce lower yields. Some potential issues include incomplete lysis and contaminants. Additional clean-up […]
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Advancements in Nanopore Sequencing for Microbial Genomics

I continued watching the “Enhanced microbial profiling and metagenomics with nanopore sequencing” webinar. The second speaker was Steven Batinovic, a Field Application Scientist with Oxford Nanopore Technologies (ONT). The title of their session was “What you’re missing matters: delivering the future of microbial genomics with Oxford Nanopore.” Batinovic started by listing the microbiology and infectious […]
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Exploring EPI2ME: Bioinformatics for Genomic Characterization

Tonight, I continued watching the ONT webinar I started last night, which focused on scalable human genomic characterization with nanopore sequencing. The second speaker was Anthony Doran, Associate Director of Bioinformatics Field Applications with Oxford Nanopore Technologies. Doran’s session was titled “Bioinformatics from beginner to production: EPI2ME, Oxford Nanopore’s data analysis platform.” ONT’s theme this […]
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Understanding Human Variation and Cancer Genomics via EPI2ME

I started watching a core webinar from Oxford Nanopore Technologies (ONT) tonight. Nick Sisneros from ONT facilitated the presentation. The topic was scalable human genomic characterization with nanopore. The first presentation was by Philipp Rescheneder, Senior Director of Applications Bioinformatics at ONT. They described three end-to-end workflows using EPI2ME: the human variation, cancer genomics, and […]
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EPI2ME 2024: Data Analysis and Genomic Tools

Jimmy Creith is a Field Applications Scientist in bioinformatics. They work with Oxford Nanopore Technologies and presented the London Calling 2024 Masterclass I watched tonight. The session title was “How to analyse your data with EPI2ME.” We will use EPI2ME in the course. Creith focused on how EPI2ME can be used for small and large […]
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Nanopore NO-MISS Workflow for Bacterial Genomes

We are going to use the Nanopore NO-MISS workflow. It will be used to sequence several microbial isolates. This is part of the Portable Genome Sequencing course. In preparation, this London Calling 2024 session seemed useful. Alex Trotter, Development Scientist, and Chris Alder, Bioinformatician, are both at Oxford Nanopore Technologies. They presented “How to sequence […]
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